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Seg Array Optimization #208

Merged
merged 48 commits into from
Apr 2, 2023
Merged

Seg Array Optimization #208

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99f7e7b
WIP seg array optimization
Dec 4, 2022
03f4f08
Rewrite combine_segments, improve construction of matrix, add test
Dec 4, 2022
e36ccbd
Add missing parameter pass through
Dec 4, 2022
bb2763c
Add dtype param
Dec 5, 2022
9be4d46
Various fixes to docstrings
Dec 5, 2022
29dfad5
Fix flake8
Dec 5, 2022
8bd9855
Add additional checks for data type
Dec 5, 2022
dec0816
Merge branch 'master' into seg_array_optimization
Dec 5, 2022
6b6c031
Fix doctets
Dec 5, 2022
e5bf9d0
Fix doctests again
Dec 5, 2022
217d00d
More fix doctests
Dec 5, 2022
761327d
Apply suggestions from code review
CPBridge Dec 6, 2022
6a4d6ec
Fix line length
Dec 7, 2022
4325153
Support more ways of specifying dtypes
Dec 7, 2022
f80fd92
Rename private function
Dec 7, 2022
d2f0513
Update src/highdicom/seg/sop.py
CPBridge Dec 7, 2022
c280d4b
Update src/highdicom/seg/sop.py
CPBridge Dec 7, 2022
d5bae73
Merge branch 'seg_array_optimization' of github.com:herrmannlab/highd…
Dec 7, 2022
2ccf9f0
Implement SQL method for source instances and source frames,
Dec 18, 2022
91e78fc
Implement get_pixels_by_dimension_index_values
Dec 19, 2022
a97b5e5
Add ORDER BY to improve cache efficiency
Dec 19, 2022
6a647f9
Undo accidental docstring edit
Jan 28, 2023
2d1752e
rename _db and add type annotation
Jan 28, 2023
b7f232f
Move to sqlite context manager
Jan 28, 2023
f81e7b6
Switch to using SOPInstanceUID directly as primary key
Jan 28, 2023
8e95876
Use max frame number to determine whether a frame number is invalid
Jan 28, 2023
6ee1031
Update user guide
Jan 28, 2023
5a8940b
Update src/highdicom/seg/sop.py
CPBridge Feb 19, 2023
f5e8c35
Update src/highdicom/seg/sop.py
CPBridge Feb 19, 2023
868039a
WIP refactoring into _SegDBManager class
CPBridge Mar 8, 2023
9e65de7
Merge branch 'seg_array_optimization' of github.com:MGHComputationalP…
CPBridge Mar 8, 2023
6956770
Complete refactor into _SegDBManager
Mar 11, 2023
8872216
Refactor using context managers to handle temp tables
Mar 11, 2023
8f5172f
Handle DB commits better
Mar 11, 2023
341e484
Improve type hints and docstrings for _SegDBManager
Mar 11, 2023
aed4213
Missing imports
Mar 11, 2023
dffd9bc
Change bone_segments -> bone_segment_numbers in user guide
CPBridge Apr 1, 2023
15782ae
Change prints to asserts in user guide
CPBridge Apr 1, 2023
24a41e3
Apply suggestions from code review
CPBridge Apr 1, 2023
820aaef
Fix text wrapping and np -> numpy in docstrings
CPBridge Apr 1, 2023
fa0c709
Remove further unnecessary temporaries like those found in code review
CPBridge Apr 1, 2023
8cda36a
Rename methods as in code review
CPBridge Apr 1, 2023
ce3a6fd
Shorten docstring
CPBridge Apr 1, 2023
281bcb8
Rename temporary table methods, add yield doc
CPBridge Apr 1, 2023
a03a957
Improve docs for _SegDBManager methods
CPBridge Apr 1, 2023
29d96f8
Further improvements to docstring
CPBridge Apr 1, 2023
1f9b9da
Clarify docstrings on the db iterators
CPBridge Apr 1, 2023
c6e5427
Fix asserts in user guide
CPBridge Apr 1, 2023
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